HEADER DE NOVO PROTEIN 07-JAN-25 9MRB TITLE THE DESIGNED SERINE HYDROLASE KNOWN AS DAD_T1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAD_T1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME, SERINE HYDROLASE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.PELLOCK,A.LAUKO,A.BERA,D.BAKER REVDAT 3 30-APR-25 9MRB 1 JRNL REVDAT 2 02-APR-25 9MRB 1 JRNL REVDAT 1 19-FEB-25 9MRB 0 JRNL AUTH A.LAUKO,S.J.PELLOCK,K.H.SUMIDA,I.ANISHCHENKO,D.JUERGENS, JRNL AUTH 2 W.AHERN,J.JEUNG,A.F.SHIDA,A.HUNT,I.KALVET,C.NORN, JRNL AUTH 3 I.R.HUMPHREYS,C.JAMIESON,R.KRISHNA,Y.KIPNIS,A.KANG, JRNL AUTH 4 E.BRACKENBROUGH,A.K.BERA,B.SANKARAN,K.N.HOUK,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF SERINE HYDROLASES. JRNL REF SCIENCE V. 388 U2454 2025 JRNL REFN ESSN 1095-9203 JRNL PMID 39946508 JRNL DOI 10.1126/SCIENCE.ADU2454 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 8173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 51.1900 - 3.6400 0.99 1255 140 0.1925 0.2389 REMARK 3 2 3.6400 - 2.8900 0.99 1227 136 0.2203 0.2410 REMARK 3 3 2.8900 - 2.5200 0.99 1222 136 0.2114 0.2511 REMARK 3 4 2.5200 - 2.2900 0.99 1231 137 0.2201 0.2798 REMARK 3 5 2.2900 - 2.1300 0.98 1201 133 0.2361 0.3178 REMARK 3 6 2.1300 - 2.0000 0.99 1219 136 0.2665 0.3125 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.815 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1162 REMARK 3 ANGLE : 0.396 1565 REMARK 3 CHIRALITY : 0.034 175 REMARK 3 PLANARITY : 0.004 201 REMARK 3 DIHEDRAL : 14.310 439 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9MRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8217 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 51.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.18520 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.49400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M POTASSIUM CHLORIDE, 0.02M TRIS REMARK 280 PH7.0, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 21.21200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.36050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.21200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.36050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 423 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 ALA A 7 REMARK 465 GLN A 8 REMARK 465 GLY A 47 REMARK 465 ASP A 48 REMARK 465 GLU A 49 REMARK 465 SER A 50 REMARK 465 LYS A 51 REMARK 465 ARG A 155 REMARK 465 ARG A 156 REMARK 465 ALA A 157 REMARK 465 ALA A 158 DBREF 9MRB A 1 158 PDB 9MRB 9MRB 1 158 SEQRES 1 A 158 MET THR GLU GLU GLU LYS ALA GLN ALA VAL GLU ASP PHE SEQRES 2 A 158 HIS LYS TYR HIS THR ALA LEU VAL VAL ARG LEU ALA GLY SEQRES 3 A 158 VAL PRO PRO HIS GLU ARG TYR GLU ARG LEU ASP ARG TRP SEQRES 4 A 158 ILE THR GLU GLN LEU ILE TYR GLY ASP GLU SER LYS ARG SEQRES 5 A 158 ASP GLU TRP ILE ASP ALA LEU ALA GLU ALA ALA GLY ILE SEQRES 6 A 158 PHE LYS GLU ALA LEU GLU ARG ASN ILE THR THR PRO GLU SEQRES 7 A 158 GLU PHE ASN ALA PHE LEU LYS GLU LYS GLY LYS ARG ALA SEQRES 8 A 158 VAL ASP LEU VAL ALA THR LEU THR ASN ALA TYR ILE ALA SEQRES 9 A 158 VAL LEU GLU GLY ASP PRO GLU ALA ILE ALA ARG PHE LEU SEQRES 10 A 158 GLY ILE SER LEU GLU GLU VAL GLN GLU ILE ILE ASP ALA SEQRES 11 A 158 ALA ARG LYS ALA VAL LYS GLU GLY ARG GLY ALA SER ILE SEQRES 12 A 158 GLY ILE TYR THR LYS LEU ARG GLU LEU GLU GLU ARG ARG SEQRES 13 A 158 ALA ALA HET PG4 A 301 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PG4 C8 H18 O5 FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 ALA A 9 GLY A 26 1 18 HELIX 2 AA2 HIS A 30 TYR A 46 1 17 HELIX 3 AA3 ASP A 53 GLU A 71 1 19 HELIX 4 AA4 THR A 76 GLY A 88 1 13 HELIX 5 AA5 GLY A 88 ASP A 109 1 22 HELIX 6 AA6 ASP A 109 GLY A 118 1 10 HELIX 7 AA7 SER A 120 GLU A 137 1 18 HELIX 8 AA8 GLY A 140 GLU A 154 1 15 CRYST1 42.424 56.721 51.595 90.00 97.23 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023572 0.000000 0.002989 0.00000 SCALE2 0.000000 0.017630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019537 0.00000 CONECT 1133 1134 CONECT 1134 1133 1135 CONECT 1135 1134 1136 CONECT 1136 1135 1137 CONECT 1137 1136 1138 CONECT 1138 1137 1139 CONECT 1139 1138 1140 CONECT 1140 1139 1141 CONECT 1141 1140 1142 CONECT 1142 1141 1143 CONECT 1143 1142 1144 CONECT 1144 1143 1145 CONECT 1145 1144 MASTER 227 0 1 8 0 0 0 6 1181 1 13 13 END